R/filter.R

In PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

#' @title Select by treatment groups (replicate block)
#'
#' @description Select phosphosites that have been quantified in a given
#' percentage of treatment groups (e.g. 0.75 as 3 out of 4 replicates)
#' in n groups.
#'
#' @author Pengyi Yang, Taiyun Kim
#'
#' @usage selectGrps(mat, grps, percent, n)
#'
#' @param mat a matrix with rows correspond to phosphosites and columns
#' correspond to samples in replicates for different treatments.
#' @param grps a string specifying the grouping (replciates).
#' @param percent a percent from 0 to 1, specifying the percentage of quantified
#'  values in any treatment group.
#' @param n an integer indicating n or more replicates pass the percentage
#' filtering for a phosphosite to be included.
#'
#' @return a filtered matrix with at least 'percent' quantification
#' in one or more conditions
#'
#' @examples
#' data('phospho.cells.Ins.sample')
#' grps = gsub('_[0-9]{1}', '', colnames(phospho.cells.Ins))
#'
#' phospho.cells.Ins.filtered <- selectGrps(phospho.cells.Ins, grps, 0.5, n=1)
#'
#' @export
#'
selectGrps <- function(mat, grps, percent, n = 1) {
    if (missing(mat))
        stop("Parameter mat is missing!")
    if (missing(grps))
        stop("Parameter grps is missing!")
    if (missing(percent))
        stop("Parameter percent is missing!")

    if (length(grps) != ncol(mat))
        stop("Length of vector grps must be equal to number of columns in mat")
    if ((percent < 0) || (percent > 1))
        stop("Parameter percent must be a numeric value between 0 and 1")


    # split the matrix by groups and organise them to a list
    tmp <- lapply(split(seq_len(ncol(mat)), grps), function(i) mat[,
        i])

    test <- do.call(cbind, lapply(tmp, function(x) {
        rowSums(!is.na(x))/ncol(x) >= percent
    }))

    mat.filtered <- mat[rowSums(test) >= n, ]

    return(mat.filtered)
}


#' @title selectTimes
#'
#' @usage selectTimes(mat, timepoint, order, percent, w)
#'
#' @param mat a matrix with rows correspond to phosphosites and columns
#' correspond to samples in replicates for different treatments.
#' @param timepoint a timepoint as factor with a length equal to the
#' number of columns of mat.
#' @param order a vector specifying the order of timepoints.
#' @param percent a percent (decimal) from 0 to 1, to filter phosphosites with
#' with missing value larger than percent per timepoint.
#' @param w a timepoint window for selection of phosphosites to remove.
#'
#' @return a filtered matrix
#'
#' @examples
#' data("phospho_liverInsTC_RUV_sample")
#' timepoint = gsub("(.*)(\\d+[ms])(.*)", "\\2",
#'                 colnames(phospho.liver.Ins.TC.ratio.RUV))
#' timepoint[which(timepoint == "0m")] = "0s"
#' timepoint = factor(timepoint)
#' timepointOrder = c("0s", "5s", "1m", "2m", "3m", "4m", "6m")
#'
#' # For demonstration purpose, we introduce missing value at 0s
#' table(timepoint)
#'
#' phospho.liver.Ins.TC.sim = phospho.liver.Ins.TC.ratio.RUV
#' rmId = which(timepoint == "0s")
#'
#' # We replace the values to NA for the first 26 (~60%) of the '0s' samples
#' # for the first 100 phosphosite as NA
#' phospho.liver.Ins.TC.sim[1:100,rmId[1:26]] = NA
#'
#' phospho.liver.Ins.TC.sim = selectTimes(phospho.liver.Ins.TC.sim,
#'                                     timepoint, timepointOrder, 0.5,
#'                                     w = length(table(timepoint)))
#'
#' # Before filtering
#' dim(phospho.liver.Ins.TC.ratio.RUV)
#' # After filtering
#' dim(phospho.liver.Ins.TC.sim)
#'
#' @export
#'
selectTimes <- function(mat, timepoint, order, percent, w = 1) {
    if (missing(mat))
        stop("Parameter mat is missing!")
    if (missing(timepoint))
        stop("Parameter timepoint is missing!")
    if (missing(order))
        stop("Parameter order is missing!")
    if (missing(percent))
        stop("Parameter percent is missing!")
    if ((percent < 0) || (percent > 1))
        stop("Parameter percent must be a numeric value between 0 and 1")

    # split the matrix by groups and organise them to a list
    tmp <- lapply(split(seq_len(ncol(mat)), timepoint), function(i) mat[,
        i])

    test <- do.call(cbind, lapply(tmp, function(x) {
        rowSums(!is.na(x))/ncol(x) >= percent
    }))[, order]

    mat.filtered <- c()
    if ((w == 1) | (w == length(order))) {
        mat.filtered <- mat[rowSums(test) >= w, ]
    } else if (w > length(order)) {
        stop("w is greater than the number of time points.
Please try a smaller w.")
    } else {
        idx <- length(order) - w + 1
        sel <- c()
        for (i in seq_len(idx)) {
            sel <- union(sel, which(rowSums(test[, i:(i + w -
                1)]) == w))
        }
        mat.filtered <- mat[sel, ]
    }

    return(mat.filtered)
}



#' @title Select phosphosite by percentage of quantification
#'
#' @description Select phosphosites that have been quantified in more than a
#' given percentage of samples
#'
#' @usage selectOverallPercent(mat, percent=NULL, n=NULL)
#'
#' @param mat a matrix with rows correspond to phosphosites and columns
#' correspond to samples in replicates for different treatments.
#' @param percent a percent from 0 to 1, specifying the percentage of quantified
#' values in across all samples for retaining a phosphosite for subsequent
#' analysis.
#' @param n an integer indicating n or more quantified values required for
#' retaining a phosphosite for subsequent analysis.
#'
#' @return a filtered matrix
#'
#' @examples
#'
#' data('phospho.cells.Ins.sample')
#'
#' phospho.cells.Ins.filtered <- selectOverallPercent(phospho.cells.Ins, 0.5)
#'
#' # Before filtering
#' dim(phospho.cells.Ins)
#' # After filtering
#' dim(phospho.cells.Ins.filtered)
#'
#' @export
#'
selectOverallPercent <- function(mat, percent = NULL, n = NULL) {
    mat.filtered <- NULL

    if (missing(mat))
        stop("Parameter mat is missing!")
    if ((!is.null(percent)) && ((percent < 0) || (percent > 1)))
        stop("Parameter percent must be a numeric value between 0 and 1")
    if (is.null(percent) & is.null(n))
        stop("specify either percentage of number of quantified values for a
given phosphosite to be retained.")

    if (!is.null(percent) & is.null(n)) {
        mat.filtered <- mat[rowSums(!is.na(mat))/ncol(mat) >=
            percent, ]
    } else if (is.null(percent) & !is.null(n)) {
        mat.filtered <- mat[rowSums(!is.na(mat)) >= n, ]
    } else {
        mat.filtered <- mat[(rowSums(!is.na(mat))/ncol(mat) >=
            percent) & (rowSums(!is.na(mat)) >= n), ]
    }
    return(mat.filtered)
}